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Detailed information for vg0517678789:

Variant ID: vg0517678789 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 17678789
Reference Allele: GAlternative Allele: T,A
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGCACACTCTTATCAACGGGTGCGTACATTGTCTACTATTGAAATAATAGTTAGAAGTAAATAAGAACACTCGTATCAAAAATAGGATTTGAATCTCTAT[G/T,A]
GGTTAGTTTCACCACAAAGAATCTAGCTAACCAGATAAGCTACGCTCACCTTACTGGTTAGATTTTTTTTTCAAGAGAATATGTCGATATTTTTTATAGT

Reverse complement sequence

ACTATAAAAAATATCGACATATTCTCTTGAAAAAAAAATCTAACCAGTAAGGTGAGCGTAGCTTATCTGGTTAGCTAGATTCTTTGTGGTGAAACTAACC[C/A,T]
ATAGAGATTCAAATCCTATTTTTGATACGAGTGTTCTTATTTACTTCTAACTATTATTTCAATAGTAGACAATGTACGCACCCGTTGATAAGAGTGTGCT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.70% 3.70% 0.47% 0.00% A: 0.08%
All Indica  2759 100.00% 0.00% 0.04% 0.00% NA
All Japonica  1512 87.00% 11.40% 1.39% 0.00% A: 0.20%
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 86.60% 11.70% 1.69% 0.00% NA
Tropical Japonica  504 97.40% 1.60% 0.60% 0.00% A: 0.40%
Japonica Intermediate  241 66.80% 30.70% 2.07% 0.00% A: 0.41%
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 3.30% 0.00% 0.00% A: 1.11%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0517678789 G -> T LOC_Os05g30510.1 upstream_gene_variant ; 1705.0bp to feature; MODIFIER silent_mutation Average:92.741; most accessible tissue: Minghui63 root, score: 97.132 N N N N
vg0517678789 G -> T LOC_Os05g30500-LOC_Os05g30510 intergenic_region ; MODIFIER silent_mutation Average:92.741; most accessible tissue: Minghui63 root, score: 97.132 N N N N
vg0517678789 G -> A LOC_Os05g30510.1 upstream_gene_variant ; 1705.0bp to feature; MODIFIER silent_mutation Average:92.741; most accessible tissue: Minghui63 root, score: 97.132 N N N N
vg0517678789 G -> A LOC_Os05g30500-LOC_Os05g30510 intergenic_region ; MODIFIER silent_mutation Average:92.741; most accessible tissue: Minghui63 root, score: 97.132 N N N N

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID Ref Alt Root (RT) Young Leaf (YL) Flag Leaf (FL) Young Panicle (YP) Lemma & Palea (LP) Stamen & Pistil (SP)
vg0517678789 G A 0.0 0.0 -0.01 0.01 0.0 0.01
vg0517678789 G T 0.0 0.01 -0.01 -0.01 0.0 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0517678789 2.14E-06 1.12E-06 mr1544_2 Jap_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0517678789 9.14E-06 NA mr1952_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251